7WWK | pdb_00007wwk

Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab

• PDB DOI: https://doi.org/10.2210/pdb7WWK/pdb
• EM Map EMD-32868: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-02-13 Released: 2023-02-15 
• Deposition Author(s): Guo, H., Gao, Y., Lu, Y., Yang, H., Ji, X.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab

Guo, H., Gao, Y., Lu, Y., Yang, H., Ji, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 94.12 kDa 
• Atom Count: 6,620 
• Modeled Residue Count: 845 
• Deposited Residue Count: 846 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], B [auth C]	194	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 15  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
55A8 light chain	C [auth F], E [auth H]	108	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
55A8 light chain	D [auth G], F [auth I]	121	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Guo, H., Gao, Y., Lu, Y., Yang, H., Ji, X.

---

Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2023-04-19
  Changes: Database references, Structure summary
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-02
  Changes: Data collection